4E6C

p38a-perifosine Complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.39 Å
  • R-Value Free: 0.292 
  • R-Value Work: 0.214 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Lipid Molecules Induce p38 alpha Activation via a Novel Molecular Switch.

Tzarum, N.Eisenberg-Domovich, Y.Gills, J.J.Dennis, P.A.Livnah, O.

(2012) J.Mol.Biol. 424: 339-353

  • DOI: 10.1016/j.jmb.2012.10.007
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • p38α mitogen-activated protein kinase (MAPK) is generally activated by dual phosphorylation but has also been shown to exhibit alternative activation modes. One of these modes included a direct interaction with phosphatidylinositol ether lipid analog ...

    p38α mitogen-activated protein kinase (MAPK) is generally activated by dual phosphorylation but has also been shown to exhibit alternative activation modes. One of these modes included a direct interaction with phosphatidylinositol ether lipid analogues (PIA) inducing p38α autoactivation and apoptosis. Perifosine, an Akt inhibitor in phase II clinical trials, also showed p38α activation properties similarly to those of PIAs. The crystal structures of p38α in complex with PIA23, PIA24 and perifosine provide insights into this unique activation mode. The activating molecules bind a unique hydrophobic binding site in the kinase C'-lobe formed in part by the MAPK insert region. In addition, there are conformational changes in the short αEF/αF loop region that acts as an activation switch, inducing autophosphorylation. Structural and biochemical characterization of the αEF/αF loop identified Trp197 as a key residue in the lipid binding and in p38α catalytic activity. The lipid binding site also accommodates hydrophobic inhibitor molecules and, thus, can serve as a novel p38α-target for specific activation or inhibition, with novel therapeutic implications.


    Organizational Affiliation

    Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences and The Wolfson Centre for Applied Structural Biology, The Hebrew University of Jerusalem, Jerusalem 91904, Israel.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Mitogen-activated protein kinase 14
A
360Homo sapiensMutation(s): 0 
Gene Names: MAPK14 (CSBP, CSBP1, CSBP2, CSPB1, MXI2, SAPK2A)
EC: 2.7.11.24
Find proteins for Q16539 (Homo sapiens)
Go to Gene View: MAPK14
Go to UniProtKB:  Q16539
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
0O8
Query on 0O8

Download SDF File 
Download CCD File 
A
(1,1-dimethylpiperidin-1-ium-4-yl) octadecyl hydrogen phosphate
PERIFOSINE
C25 H53 N O4 P
SZFPYBIJACMNJV-UHFFFAOYSA-O
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
0O8Kd: ~15000 nM BINDINGMOAD
0O8Kd: 15000 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.39 Å
  • R-Value Free: 0.292 
  • R-Value Work: 0.214 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 68.022α = 90.00
b = 74.031β = 90.00
c = 74.447γ = 90.00
Software Package:
Software NamePurpose
MOLREPphasing
SCALEPACKdata scaling
REFMACrefinement
HKL-2000data reduction
HKL-2000data collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-10-31
    Type: Initial release
  • Version 1.1: 2013-02-13
    Type: Non-polymer description
  • Version 1.2: 2013-06-19
    Type: Database references
  • Version 1.3: 2018-01-24
    Type: Structure summary